def test_too_small_k(self):
a = probe.Probe.from_str('ABCDEFGHIJ')
b = probe.Probe.from_str('ZYXWVUTSRQ')
probes = [a, b]
with self.assertRaises(probe.PigeonholeRequiresTooSmallKmerSizeError):
# Should pick k=5, but requires k=6
probe._construct_pigeonholed_kmer_probe_map(probes, 1, min_k=6)
with self.assertRaises(probe.PigeonholeRequiresTooSmallKmerSizeError):
# Should pick k=2, but requires k=3
probe._construct_pigeonholed_kmer_probe_map(probes, 3, min_k=3)
def test_pigeonholed_kmer_map(self):
a = probe.Probe.from_str('ABCDEFGH')
b = probe.Probe.from_str('ZYXWVUAB')
probes = [a, b]
kmer_map = probe._construct_pigeonholed_kmer_probe_map(
probes, 3, min_k=2, include_positions=True)
shared_kmer_map = probe.SharedKmerProbeMap.construct(kmer_map)
# Should pick k=2
a_str = a.seq_str
b_str = b.seq_str
self.assertEqual(len(kmer_map), 7)
self.assertCountEqual(shared_kmer_map.get('AB'),
[(a_str, 0), (b_str, 6)])
self.assertCountEqual(shared_kmer_map.get('CD'),
[(a_str, 2)])
self.assertCountEqual(shared_kmer_map.get('EF'),
[(a_str, 4)])
self.assertCountEqual(shared_kmer_map.get('GH'),
[(a_str, 6)])
self.assertCountEqual(shared_kmer_map.get('ZY'),
[(b_str, 0)])
self.assertCountEqual(shared_kmer_map.get('XW'),
[(b_str, 2)])
self.assertCountEqual(shared_kmer_map.get('VU'),
[(b_str, 4)])
self.assertIsNone(shared_kmer_map.get('MN'))
self.assertEqual(shared_kmer_map.k, 2)
def test_shared_kmer(self):
a = probe.Probe.from_str('ABCDEFGHIJ')
b = probe.Probe.from_str('ZYXWVABCDE')
probes = [a, b]
kmer_map = probe._construct_pigeonholed_kmer_probe_map(
probes, 1, min_k=2)
# Should pick k=5
self.assertEqual(len(kmer_map), 3)
self.assertCountEqual(kmer_map['ABCDE'], [a, b])
self.assertCountEqual(kmer_map['FGHIJ'], [a])
self.assertCountEqual(kmer_map['ZYXWV'], [b])
def test_no_mismatches(self):
a = probe.Probe.from_str('ABCDEFGHIJ')
b = probe.Probe.from_str('ZYXWVUTSRQ')
probes = [a, b]
kmer_map = probe._construct_pigeonholed_kmer_probe_map(
probes, 0, min_k=5)
# k-mers equal to the full length of the probe should be
# chosen
self.assertTrue(a in kmer_map[a.seq_str])
self.assertTrue(b in kmer_map[b.seq_str])
self.assertFalse(a in kmer_map[b.seq_str])
self.assertFalse(b in kmer_map[a.seq_str])
def test_positions(self):
a = probe.Probe.from_str('ABCDEFGH')
b = probe.Probe.from_str('ZYXWVUAB')
probes = [a, b]
kmer_map = probe._construct_pigeonholed_kmer_probe_map(
probes, 3, min_k=2, include_positions=True)
# Should pick k=2
self.assertEqual(len(kmer_map), 7)
self.assertCountEqual(kmer_map['AB'], [(a, 0), (b, 6)])
self.assertCountEqual(kmer_map['CD'], [(a, 2)])
self.assertCountEqual(kmer_map['EF'], [(a, 4)])
self.assertCountEqual(kmer_map['GH'], [(a, 6)])
self.assertCountEqual(kmer_map['ZY'], [(b, 0)])
self.assertCountEqual(kmer_map['XW'], [(b, 2)])
self.assertCountEqual(kmer_map['VU'], [(b, 4)])
